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Detailed information for vg0137934558:

Variant ID: vg0137934558 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37934558
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GATCTATAGCCAGTTGCAGCACGGACTCCAAGACGCAATGTGTGTATGACATGGGGGACTATATATTAATAGTATAGTAAGCAACTATTATATGAATTGG[C/T]
TATAAATGAATTGGAGGCAGTAGTAGGCTATATTATTAAACTTGCTCTTATATTATAGGACGGATGGAGTAGGCAGCAACATCATACTCCCTCCATACTC

Reverse complement sequence

GAGTATGGAGGGAGTATGATGTTGCTGCCTACTCCATCCGTCCTATAATATAAGAGCAAGTTTAATAATATAGCCTACTACTGCCTCCAATTCATTTATA[G/A]
CCAATTCATATAATAGTTGCTTACTATACTATTAATATATAGTCCCCCATGTCATACACACATTGCGTCTTGGAGTCCGTGCTGCAACTGGCTATAGATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.30% 23.20% 0.57% 0.00% NA
All Indica  2759 67.60% 31.90% 0.54% 0.00% NA
All Japonica  1512 98.70% 0.50% 0.73% 0.00% NA
Aus  269 27.10% 72.50% 0.37% 0.00% NA
Indica I  595 63.70% 36.00% 0.34% 0.00% NA
Indica II  465 85.80% 13.30% 0.86% 0.00% NA
Indica III  913 54.80% 45.10% 0.11% 0.00% NA
Indica Intermediate  786 74.70% 24.30% 1.02% 0.00% NA
Temperate Japonica  767 98.00% 0.50% 1.43% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0137934558 C -> T LOC_Os01g65370.1 downstream_gene_variant ; 1263.0bp to feature; MODIFIER silent_mutation Average:76.714; most accessible tissue: Minghui63 flower, score: 92.509 N N N N
vg0137934558 C -> T LOC_Os01g65370-LOC_Os01g65380 intergenic_region ; MODIFIER silent_mutation Average:76.714; most accessible tissue: Minghui63 flower, score: 92.509 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0137934558 C T 0.02 -0.05 -0.04 -0.02 -0.05 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137934558 8.44E-07 NA mr1134 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 3.04E-07 NA mr1517 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 1.11E-12 1.34E-14 mr1517 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 2.51E-07 NA mr1538 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 7.37E-11 3.47E-12 mr1538 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 6.64E-06 NA mr1134_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 9.88E-06 2.21E-06 mr1134_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 4.61E-08 NA mr1517_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 1.31E-13 2.25E-13 mr1517_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 3.13E-06 NA mr1538_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0137934558 1.46E-10 1.45E-13 mr1538_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251